Package: TiPS
Type: Package
Title: Trajectories and Phylogenies Simulator
Version: 1.3.0
Date: 2025-05-05
Authors@R: c(person("Gonche", "Danesh", role = c("aut", "cre", "cph"), email = "gonche.danesh@gmail.com"),
	     person("Emma", "Saulnier", role = c("aut", "cph")),
			 person("Olivier", "Gascuel", role = c("aut", "cph")),
	     person("Marc", "Choisy", role = c("aut", "cph", "ths")),
	     person("Samuel", "Alizon", role = c("aut", "cph", "ths")))
Maintainer: Gonche Danesh <gonche.danesh@gmail.com>
Description: Generates stochastic time series and genealogies associated with a population dynamics model. Times series are simulated using the Gillespie exact and approximate algorithms and a new algorithm we introduce that uses both approaches to optimize the time execution of the simulations. Genealogies are simulated from a trajectory using a backwards-in-time based approach. Methods are described in Danesh G et al (2022) <doi:10.1111/2041-210X.14038>.
License: GPL (>= 2)
Depends: R (>= 4.0.0)
Imports: graphics, grDevices, gtools, inline, methods, Rcpp (>=
        0.12.14), stats, stringr, utils
Suggests: knitr, rmarkdown, ape, testthat (>= 3.0.0)
LinkingTo: Rcpp, BH
VignetteBuilder: knitr
NeedsCompilation: yes
RoxygenNote: 7.1.1
Encoding: UTF-8
BugReports: https://gitlab.in2p3.fr/ete/tips/-/issues
URL: https://gitlab.in2p3.fr/ete/tips/
Config/testthat/edition: 3
Author: Gonche Danesh [aut, cre, cph],
  Emma Saulnier [aut, cph],
  Olivier Gascuel [aut, cph],
  Marc Choisy [aut, cph, ths],
  Samuel Alizon [aut, cph, ths]
Repository: CRAN
Packaged: 2025-05-09 10:21:40 UTC; g.danesh
Date/Publication: 2025-05-09 12:50:02 UTC
Built: R 4.4.3; x86_64-w64-mingw32; 2026-04-15 03:22:53 UTC; windows
Archs: x64
